In 1992 he accepted a Fulbright professorship at the University of Cluj-Napoca, Romania. There, together with a few underground Romanian activists, he became deeply involved in campaigning against Article 200 of the Romanian penal code, a law dating from the Ceauşescu dictatorship that criminalized consensual homosexual acts with five years' imprisonment. Working independently from any institution, Long visited dozens of Romanian prisons over the following years, interviewing prisoners, linking them to legal assistance, and documenting torture and arbitrary arrest of lesbians as well as gay men. He identified some of the first lesbians and gay men taken up as prisoners of conscience by Amnesty International. His documentation was crucial in persuading the Council of Europe to strengthen its stand on lesbian and gay issues, and to demand that Romania repeal its sodomy law. He was a founding member of the Romanian gay and lesbian organization Accept. His work spearheaded a European campaign and contributed strongly to Romania's eventual repeal of Article 200 in 2001.[8]

In 1993 Long conducted the first human-rights mission to Albania to meet with gay activists there, and his documentation of arrests and abuses helped lead to the repeal of that country's sodomy law.

Long also led IGLHRC's advocacy at the groundbreaking 2001 United NationsGeneral Assembly Special Session on HIV/AIDS. IGLHRC was invited to address the session, then blocked by conservative Islamic states and the Holy See. The crisis led to the first-ever General Assembly vote on a gay/lesbian issue, which resulted in a victory and in IGLHRC's reinstatement.

In 2002, Long left IGLHRC for Human Rights Watch, the largest U.S.-based human rights organization, where he was mandated to create a program on lesbian, gay, bisexual, and transgender rights—the first such program in a major, "mainstream" human rights organization. The program was formally launched in 2004. From 2001, Long had been deeply engaged in combating a crackdown on homosexual conduct in Egypt.[9] In May 2001, police in Cairo raided a floating Nile discothèque called the Queen Boat, arresting dozens of men and staging a show trial for "blasphemy" as well as "debauchery."[10] Long attended and reported on their trial. In succeeding months, hundreds, possibly thousands of other men were arrested in raids and through Internetentrapment. Long spent months in Egypt in 2003 documenting the extent of the crackdown.[11] Working for Human Rights Watch, he also documented a brutal government assault on anti-war activists, Islamists, and the political Left. The bridges he thus built helped persuade parts of Egypt's human rights community to take lesbian and gay issues within their work.

In 2004, together with Human Rights Watch executive director Kenneth Roth, Long launched a report on the Egyptian crackdown against gays, in Cairo, accompanied and supported by five Egyptian human rights groups. From the day the report was released, arrests for homosexual conduct in Egypt stopped. According to Long, a prominent contact in Egypt's Interior Ministry said, "It is the end of the gay cases in Egypt, because of the activities of certain human rights organizations."[12]

Later in 2004, Long worked to launch a Human Rights Watch report on homophobic violence and HIV/AIDS in Jamaica. The report stimulated an intense debate in Jamaica and across the Caribbean over homosexuality and the region's colonial-era sodomy laws, a furious controversy which continued for over a year. Editorials condemning Jamaica's anti-gay policies appeared in publications such as The New York Times and The Economist, and filled the Jamaican press as well. For the first time the government suggested a willingness to modify its repressive legislation on consensual sexual acts.

In 2006, Long was the principal author of a report on binational same-sex couples and the discrimination they face in U.S. immigration law, amid a fierce religious and social backlash against recognition of same-sex relationships in the United States

Long also went to Moscow in 2006 to support Russian activists, including Nikolay Alexeyev, attempting to organize a gay pride march in the face of an official ban. The ban was part of a general strangling of civil society as President Vladimir Putin's rule became more authoritarian. Long witnessed and reported on skinhead and police violence against marchers, including a brutal attack on German member of the BundestagVolker Beck.[13]

Long's work produced controversy in 2005 and 2006 after the hanging of two teenagers in the city of Mashhad, Iran. Some gay activists in the West insisted that the youths were hanged not for the rape of a 13-year-old (as initially reported in the Iranian press) but for being gay. Long and Human Rights Watch, while condemning the executions and conducting intensive research on the situation for LGBT people in Iran, maintained that the evidence in the Mashhad case was inconclusive, and also questioned the attribution of a Western "gay" identity in culturally complex situations. Long was attacked for an overly-theoretical approach to political activism. Some questioned whether his work reflected a covertly pro-Islamic stance.[14]

At a time when Islamic states routinely punish consensual homosexuality involving youths with long prison terms, Long also has been criticized for embracing a narrow understanding of gay identity that ignores these attacks on same-sex activity.[15]

Long was Executive Director of the Lesbian, Gay, Bisexual, and Transgender Rights Program at Human Rights Watch, and resigned for "personal reasons" in August 2010.[16] His resignation came shortly after HRW and Long offered an apology to Peter Tatchell for a five-year series of essays by Long in the journal Contemporary Politics which had, among other allegations, alleged that Tatchell had claimed that Asgari and Marhoni had been "wanting the rape." Tatchell accepted the apology, but American journalist for Gay City NewsDoug Ireland had eviscerated Long for years of accusations made by Long against Ireland, Tatchell, Louis-Georges Tin, Arsham Parsi and Ali Hili.[17] However, the resignation was due to illness [18] and the apology made to spare Human Rights Watch litigation in the UK.[19]